The growing number of applications of ionic liquids (ILs) in industry have brought attention to the green credentials of synthesis, as well as their cytotoxicities and ecotoxicities both for their use and accidental leakage into the environment. With the abovementioned properties in mind, we designed a class of ILs with either cations bearing a gluconamide motif and aliphatic side chains or the anion incorporating a gluconic acid (derived from food waste) moiety. An IL with an imidazolium cation with an appended gluconic amide (bearing five hydroxyl groups) moiety was also synthesized for a useful comparison. Different structural features were considered, placing emphasis on the nature and length of the alkyl chain and the nature of the anion. For comparison, two ILs, one with a hydroxyl group and another without any hydroxyl groups, were prepared. Apart from the typical characterization of ILs, such as differential scanning calorimetry, thermogravimetric analysis, conductivity, and viscosity measurements, the main focus was placed on the evaluation of their cytotoxicities and ecotoxicities, performing tests with three cancer cell lines (HeLa, HTC-116, and MCF-7) and fish embryos (zebrafish). Data obtained have shed light on the relationship working between the physicochemical properties and the structural features of the ILs. Interestingly, these ILs are able to inhibit cell growth only at very high concentrations (IC50 ≈ 10–3 M) and they do not affect the vitality of fish embryos, allowing them to be classified as harmless solvents. To our surprise, the data collected show that derivatization with the “sweet” residue on the imidazolium cation completely removes the well-known toxicity effects of imidazolium ILs.